September 2017 - galaxy-dev - lists.galaxyproject.org

upload file format is data - type not recognized in galaxy
by Pavel Fibich 26 Sep '17

26 Sep '17

Hello, do you have any idea why my galaxy 16.07 stop recognizing uploaded files and format of uploaded files is set to the format 'data'? After using older version of database backup, galaxy stop recognizing format of uploaded files (e.g. fasta, fastqc) and everything is set to format 'data'. Uploaded files are OK, I have tested them on other public galaxy servers, where they were recognized well. Before changing database (after the technical problems with the server), recognizing of the files were OK. Even in debugging level I do not see any errors or problems in the log (I have compared logs before changing database with new ones, and there are no differences). From the investigating of upload.py, I guess something happen with galaxy.datatypes.registry (settings and code of galaxy were not changed). Do you have any ideas? I cannot switch the database back and changing file format in Edit attributes is annoying. Best, Pavel

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Question about "reference_fasta_filename" for "Map with BWA" (existing tool)
by Qian, Yingzhi 22 Sep '17

22 Sep '17

Hi there, This is my first time writing to the mailing list. Thanks in advance. I want to use Map with BWA for short reads https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=25bdd3… (I have added the lines in PS (below) to the section I made in config/tool_conf.xml file and "Map with BWA" is showing up on galaxy interface when I execute run.sh. ) However, I can't pick a genome in the "Using reference genome" box. The drop-down box doesn't work. I have loaded genomes and created indexes to my local galaxy. I just don't know where to insert the path in this file - shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml> I see it has "reference_fasta_filename" (reference genome) but I am not sure what it is directing to or what to modify to tell where I put the genomes. Or is there something else I need to do? Regards, Ying PS <tool file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml>" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2>"> <tool_shed>toolshed.g2.bx.psu.edu<http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>bwa</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>051eba708f43</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2></id> <version>0.7.15.2</version> </tool>

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Displaying tool select list according to user
by Laure QUINTRIC 22 Sep '17

22 Sep '17

Hello Galaxy users, I try to figure out how I can display a select list into a galaxy tool according to the connected user. I have several .loc files containing the paths for custom blast databases I have created for several users (user1.loc, user2.loc, and so on). I would like the blast tool to display the specific databases for the connected user (user1 or user2). Any idea on how to proceed ? Regards, Laure

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galaxy behind firewall
by Matthias Bernt 19 Sep '17

19 Sep '17

Dear list, our galaxy is behind a firewall which seems to imply that many of the nice possibilities to use online services which download data from galaxy do not work, e.g. phinch or the UCSC browser. Has anybody ideas for (or experience with) workarounds? For instance, we have a local own cloud which we might exploit, i.e., upload the data to OC and modify the link. Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Deprecation of Sample Tracking and External Services
by Aysam Guerler 14 Sep '17

14 Sep '17

Hello everyone, We are considering to deprecate the Sample Tracking feature in Galaxy 18.01. Please let us know if you are using it so we can discuss alternative options. Thanks, Sam

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Dependencies issue with tool installation via ephemeris
by RMSe17 14 Sep '17

14 Sep '17

Hello, I got a new Galaxy install using 17.01 latest. I wanted to get the same tools as are in Galaxy main. I installed ephemeris with pip, used get-tool-list to get a yml file with tools, and then shed-install to my Galaxy server. After a few hours, 452 tools got successfully installed, 0 skipped and 0 errored. However, when looking at Galaxy's "manage installed tools", all of the tools that have dependencies are in gray state - missing dependencies. (and error out if ran). If I select a tool, and go to "repository actions", "manage tool dependencies", I see that dependencies are marked as never installed. If I select dependencies and click install, they install - really fast (too fast?), and then that tool works fine... but I'm trying to avoid manually telling each tool to install dependencies - there are a lot of them :) Any suggestions?

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tool runtimes
by Matthias Bernt 13 Sep '17

13 Sep '17

Dear list, I have the impression that on our cluster the "auxiliary" computations (e.g. setting metadata) is very slow (minutes) compared to the run time of the actual tools (often just seconds). Do you have any suggestion how I can tweak this or how I can analyze this more detailed? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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September Galaxy Newsletter
by Dave Clements 06 Sep '17

06 Sep '17

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installation/conda problems
by Matthias Bernt 06 Sep '17

06 Sep '17

Dear list, I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened. I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error: ``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ``` Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed): ``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ``` Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Issues with new galaxy and galaxy_lib
by Evan Clark 04 Sep '17

04 Sep '17

Is there a way to change the location of the galaxy lib directory? We migrated our galaxy and it is looking for the lib on the wrong location. Additionally this is causing errors like the one below the first error. galaxy.jobs.runners DEBUG 2017-09-01 09:35:13,673 executing external set_meta script for job 13: GALAXY_LIB="/var/web_services/galaxy/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="/var/web_services/galaxy/.venv"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python "/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/set_metadata_7mPxU0.py" "/mnt/ceph/home/galaxy/galaxy/scratch/tmpEn3vYB" "/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/working/galaxy.json" "/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/metadata_in_HistoryDatasetAssociation_13_WlHC7F,/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/metadata_kwds_HistoryDatasetAssociation_13_w_LWxj,/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/metadata_out_HistoryDatasetAssociation_13_Wjmehj,/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/metadata_results_HistoryDatasetAssociation_13_r2SVjv,/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/galaxy_dataset_13.dat,/mnt/ceph/home/galaxy/galaxy/scratch/jobs_directory/000/13/metadata_override_HistoryDatasetAssociation_13_OXLKhY" 5242880 edu/koko/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:48.0) Gecko/ Firefox/48.0" galaxy.jobs.runners DEBUG 2017-09-03 15:33:54,164 execution of external set_meta for job 19 finished galaxy.jobs.output_checker DEBUG 2017-09-03 15:33:54,241 Tool produced standard error failing job - [Traceback (most recent call last): File "/mnt/ceph/home/galaxy/galaxy/tools/data_source/upload.py", line 19, in <module> from galaxy import util ImportError: No module named galaxy ]

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